Approach:
The USDA SIV Surveillance System was initiated in 2009 and roughly 600 swine influenza virus (SIV) isolates have entered into the system. Currently, 3 gene segments (HA, NA, and M) are being sequenced routinely by participating National Animal Health Laboratory Network (NAHLN, APHIS) laboratories and the sequences submitted to the GenBank database. Approximately 150 isolates have the 3 gene sequences deposited (December 2011). There has not been a systematic approach for analyzing and reporting summarized results of the sequencing efforts on a single gene or whole virus genome level. This is a gap in providing a useful output from the surveillance system for determination of significant virus evolution and identification of viruses of interest. Additionally, the National Veterinary Services Laboratories (NVSL), APHIS-VS, will conduct whole virus sequencing on approximately 600 viruses currently in the SIV repository using the Illumina-based approach developed at St. Jude Children’s Research Hospital and adapted at the National Animal Disease Center (NADC), ARS. The NADC will be instrumental in transferring this technique to NVSL for use at the Iowa State University (ISU) Sequencing and Synthesis core facility. Preliminary data generated from the Illumina sequencing run will be initially assessed and assembled at NADC with subsequent transfer of the bioinformatics methods developed by the NADC to APHIS-VS personnel. The ISU will then perform computational evolutionary biology analyses in the context of contemporary and historical SIV for determination of phylogenetic relationships, lineages, and reassortment. Identifying the relative representation of subtypes, phylogenetic types, and whole genome variants in the swine population in geographic and temporal contexts will allow monitoring of the genetic evolution of IAV in swine. The resulting data will provide a scientific based approaches for IAV intervention strategies, vaccine and diagnostic test development, and pandemic preparedness. From the sequence analysis, novel viruses will be selected for associated in vitro and in vivo study of SIV isolates. Additionally, influenza A virus isolates may be identified through public health investigations of zoonotic transmission events or from the animal health sector for unusual phenotypes or evasion of vaccine immunity. The studies funded in this interagency agreement include in vivo and in vitro pathogenesis and transmission, antigenic characterization, or vaccine protection experiments.